36C24120Q0540 – Sources Sought – AN73–HUMAN RNA SEQUENCING SERVICES

Aug 17, 2020 | Sources Sought


This is a Sources Sought Notice with regards to the following Statement of Work:

This information will be used for solicitation planning purposes only. No quotes are being requested or accepted at this time. This is not a solicitation and no contract shall be awarded from this Sources Sought Notice.

In accordance with Public Law 109-461, the Department of Veterans Affairs is particularly interested in Service Disabled Veteran Owned Small Business (SDVOSB) and/or Veteran Owned Small Businesses (VOSB) that are interested. Interested parties responding to this Notice should submit the following information:

company name and address, point of contact with phone number, and DUNS number;
company socio-economic status to identify business as being an SDVOSB, VOSB, Small Business, Hubzone, 8a, Woman Owned, etc. Primary NAICS for this procurement will be 541715 (Research and Development in the Physical, Engineering, and Life Sciences) with a small business size standard of 1,000 employees;
Statement of capability;
if an SDVOSB or VOSB, provide proof of registration in the VA Vet Biz website and verification by VA Center for Veterans Enterprise (CVE) or intention of registration prior to submission of offers to a solicitation;
all interested firms must be registered in SAM (www.sam.gov);
all interested SDVOSB or VOSB firms must be registered in VETBIZ.GOV and Verified by VA CVE and registered in SAM to be eligible for award of Government contracts; and
any other pertinent company documentation.

The response date to this Notice is August 20, 2020, at 11:00 AM EST.

ELECTRONIC SUBMISSIONS ONLY to be sent to: anna.norcross@va.gov.


Title of Projects: PTSD-associated gene expression in the bed nucleus of the stria terminalis (BNST).

Scope of Work: The Vendor will use next-generation sequencing and RNAseq techniques to create a gene expression profile of the BNST in 100 samples from the PTSD Brain bank. They will receive RNA samples from the lab which extracted the BNST, measure sample quality, perform next generation sequencing, and provide output files to which will be returned to Dr. Mark Logue who will use these to look for gene expression signatures of PTSD and depression in the BNST region of the brain.
Background: Dr. Mark Logue currently has a VA Merit award to study the genetics and epigenetics of PTSD. As part of this project he has studied pre-frontal cortex tissue from the PTSD brain bank and found evidence of the involvement of immune system genes and oligodendrocytes in PTSD pathogenesis. This project would extend this work to the BNST which plays a role in HPA axis activation, and is activated both in chronic states of threat response and heightened awareness (anxiety) and to more acute and immediate threats (fear).

Performance Period and Type of Contract: The resulting Non-personal Services contract will have a Base Year with 1 anticipated annual option year.

Description of Requirements and Associated Deliverables:. The Vendor shall perform services utilizing equipment and methodology best suited for desired results. The need for reproducibility and follow-on to previous work which is why the Government desires the following methods, procedures, and equipment be used.

The first step is to quantify the quality of the RNAseq samples:
Assessing RNA integrity by Agilent Tapestation and concentration by Qubit assay.
Assessing library size on the Agilent Tapestation, concentration by Qubit assay, and final quantitation by qPCR
The next step is to remove ribosomal RNA through the use of Ribo-Zero depletion.
Then, RNA will be sequenced using the Illumina HiSeq, 2x150bp configuration, single index, ~350M raw paired-end reads per lane for a target coverage of 50 million reads per sample. It is guaranteed that 80% of bases Q30
The RIN values, raw FASTQ files summarizing all of the read information will be returned to Dr. Logue using a secure method.

Results of each test (deliverable) will be provided within 60 days of completion of the step. If for any reason any deliverable cannot be delivered within the scheduled time frame, the Vendor is required to explain why in writing to the Contracting Officer, including a firm commitment of when the work shall be completed.  This notice to the CO shall cite the reasons for the delay, and the impact on the overall project.  The CO will then review the facts and issue a response, in accordance with applicable regulations.

Any changes to this SOW shall be authorized and approved only through written correspondence from the CO.  A copy of each change will be kept in a project folder along with all other products of the project.  Costs incurred by the Vendor through the actions of parties other than the CO shall be borne by the Vendor.

As requested by Government but no less than once per annual performance period, provide a written report that includes:
Test results with interpretation and comment.
Information pertaining to quality control.
Provide telephone support discussing/clarifying test results with Government as may be required/requested.

Results of this work shall be available via encrypted hard drive or thumb drive or via email. The report may be in either Word format or PowerPoint format. Delivery of the report may be via upload to a Government issued encrypted thumb drive entrusted to the VA Principal Investigator to be picked up at the Vendor s location or via email direct to the VA Principal Investigator. 
This work does not involve VA human subjects data or biospecimens. It is a molecular follow-up to better understand the significance of prior results identified in the principal investigator s lab.

No travel reimbursements will be made under this contract.

Government will collaborate with the Vendor regarding additional SNPs of interest that are identified in the principal investigator s research.   

Laboratory and associated personnel shall be qualified to run the required assays and certified in accordance with all applicable laws and regulations.

Without the express written consent of the Government, results of this Scope of Work may not be used by the Vendor in grant applications, scientific publications or presentations until such a time as the results are published by the Government in a peer review journal.

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